In the Autumn of 2024, I enrolled in PhD studies at the Faculty of Organizational Sciences, Belgrade University. In the meantime, I’ve been working on different subjects and research projects.
A particularly challenging one has been a scientific article for a peer-reviewed journal I’ve been working on with my mentor. As of now, there are 50+ references we cite, and my old workflow for academic writing & citing failed. There was simply way too many folders, pdf files, notes, and moving parts for a very manual process I used to do. Too much time used and too many points of failure/possible errors. (Initial feedback on the article was positive, and we’re communicating with an interested peer-reviewed journal – BUT they also underlined there have been some minor errors in references.)
So, the system needed to evolve.
I’ve been on the lookout for tools and workflows that could help, and everything sort of fell into place recently. A friend recommended Zotero, and members of a few online communities for knowledge workers suggested useful plugins for Zotero and Obsidian to make them work together, I had a few ideas… and soon enough there was the new flow.
Tools
- Zotero – free tool for research organizing, citing, and more
- Obsidian – free, flexible note-taking app with a large community and a heavy reliance on open standards (which makes it future-proof)
- MS Word – still the gold standard for more formal writing, there seems to be a free cloud version (personally, I have Office 365 subscription)
- Apple notes – free within the Apple ecosysten, ideal for quick notes on the go
*Available for other word processors such as LibreOffice or Google docs, so you can easily swap out MS Word or use the setup with multiple word processors
The Process and Core Elements
When I find a new resource, I either add it to Zotero right away, along with metadata (Author, Date, Publisher, DOI or ISBN etc.), or I quickly save it to Apple Notes temporarily, to be added to Zotero later.
Once a resource is added to Zotero, a folder is created automatically within Obsidian, where I open an Obsidian note (in markdown) related to the resource.
If available, the digital copy of the resource is stored in the folder (e.g. article pdf).
Once a resource is in the system (Zotero + Obsidian), I:
- use Zotero for adding citations and bibliography* to Word documents.
- use Obsidian as usual for managin my notes and linking them to each other (or digital files/resources)
Zotero has notes feature, but I didn’t try it out and prefer to have notes in markdown within Obsidian – which makes them future-proof. If Obsidian or Zotero are gone, a popular open format like markdown will likely be easily used in another program. (note: I did not research exporting from Zotero; maybe it’s not difficult.)
I like MS Word for the final piece as it’s the de facto gold standard for submitting articles and similar. Zotero makes it super easy to add references and generate a bibliography (imagine having 50+ references you have to manually write down). Obsidian is great for personal knowlegde management (PKM).
So, I use each tool for what they are best:
- Obsidian -> PKM
- Zotero -> Citation
- Word -> Final writing
Conclusion & Some Further Reading
I’m very happy with the v2 of the workflow, but it will most likely evolve further as I use it more. I’ll write an update once there are meaningful changes/improvements.
Are you curious about academic writing and note-taking / PKM?
Check out:
- Nesslabs – Initially a PKM and note-taking community, now a space for experimenting and mindful productivity
- The Effortless Academic – courses for using AI and different digital tools for research (lit review, writing, publishing…)
- Build a Second Brain – PKM by Tiago Forte
A Practical Guide to setting up v2?
If you’re curious about setting up the system in practice, let me know. If there are no people interested in it, I will not write the guide 🙂
Featured image created using GenAI